Waller has struck 13 fours off 88 deliveries, with Pakistan-born Sikandar Raza giving him company on 29 off 79 deliveries with four fours.
They have added 95 runs in their unbroken fourth-wicket stand at Harare Sports Club.
Opener Vusi Sibanda (31) and captain Hamilton Masakadza (19) earlier steadied Zimbabwe with a 48-run, second-wicket partnership after the early loss of Tino Mawoyo but their dismissals off successive deliveries undid the good work.
Sibanda was out off the last ball of a Khan over and Masakadza was bowled off the first ball of a new over from offspinner Saeed Ajmal as the batsman played inside the line of a delivery and lost his off stump.
For Pakistan, Khan took 2-29 on a pitch that did not have much for the bowlers on the second day.
Earlier, Pakistan failed to add to its overnight score of 249-9 as Ajmal was bowled by pace bowler Tendai Chatara for 49, one short of his career-best score.
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